Biotechnology: Using DNA origami to solve mathematical problems

A DNA-based calculator that takes two inputs - encoded in DNA strands - and returns the result of their multiplication, showing this as a number on a display, is described in Nature Communications this week. Biological systems generate a huge amount of information that requires a flexible method of analysis. Using DNA to take input values and rapidly deliver a usable answer is one way of making sense of this volume of data.

DNA can encode non-genetic information into its nucleotide sequence, allowing multiple calculations to be performed at once through the simultaneous interaction of thousands of DNA molecules. Most currently available DNA-based computing systems work by mimicking electronic computers (through the design of so-called ‘logic gates’ that perform operations).

Kurt Vesterager Gothelf and colleagues design a DNA ‘look up table’ that can take two input values encoded in DNA and find an answer by looking through a library of possible answers. They design sets of single stranded DNA oligonucleotides that can bind together to form a ‘question’ - such as ‘2 x 2’ - and correctly bind to an ‘answer’ strand of DNA, creating a four stranded DNA origami structure. The answer can be read because the DNA structure binds to a specifically-designed microarray that transmits the information to a visual readout.

Although this calculator does not yet have a practical application, the authors suggest it could be used to aid biosensing and synthetic biology-based regulatory systems. With further development, it may eventually be used as a diagnostic device, which would take disease-specific nucleic acids as inputs and retrieve an answer coded in DNA from a pool of possibilities.